From Sanford Underground Research Facility: “A case study in happy extremophiles”

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From Sanford Underground Research Facility

July 19, 2019
Erin Broberg

Petri plate with colonies of a methanotrophic microorganism. Photo courtesy Christopher Abin

If asked to describe your ideal environment, the odds are you wouldn’t opt for somewhere exceedingly salty, with an acidic pH or a dense supply of methane. However, some organisms (with fewer cells and vastly different standards than you and me) would say that sounds just about perfect.

Researchers recently visited Sanford Underground Research Facility (Sanford Lab) to collect samples of organisms that prefer the damp, dark environment of the deep subsurface. Now, they are trying to replicate those seemingly abysmal conditions back in their laboratory. By providing the perfect conditions, researchers can selectively grow the bacteria they want to study.

BuG ReMeDee researchers before their descent to the 4850 Level of Sanford Lab. Left to right: Roland Hatzenpichler, professor at Montana State University; Mackenzie Lynes, graduate student at Montana State University; Christopher Abin, postdoc at the University of Oklahoma; Christopher Garner, graduate student at OU; and Rosie Moon-Escamilla, graduate student at OU.

This research is part of the National Science Foundation’s (NSF) BuG ReMeDee project (Building Genome-to-Phenome Infrastructure for Regulating Methane in Deep and Extreme Environments). This collaborative group of researchers from three universities is seeking to understand curious life forms called methanotrophs—organisms that survive by consuming methane.

“Much of the general public looks at bacteria like germs, like something harmful,” said Christopher Abin, postdoctoral researcher at the University of Oklahoma. “But what we see is that the vast majority of bacteria are incredibly important—without them, the earth wouldn’t really function properly. In fact, life on earth would cease to exist without bacteria.”

In the effort to understand and utilize the creatures that feast on a greenhouse gas more potent than carbon dioxide, each collaborating university has their niche.

At South Dakota School of Mines & Technology (SD Mines), principal investigator Rajesh Sani’s team focuses on genetically engineering and improving methane-consuming microbes to create useable products and materials, such as biofuels, biodegradable plastics or electricity. At Montana State University (MSU), Robin Gerlach’s team is developing models that show how microbes consume methane and create energy. This helps scientists better understand how methane generated under such places as Yellowstone National Park and other geothermal environments and fossil fuel beds impacts our climate.

But before models can be made and genes engineered, researchers need a solid understanding of how these organisms function. To study them in detail, researchers from the University of Oklahoma (OU) and under the lead of Lee Krumholz, collect and cultivate samples, isolating pure cultures of methanotrophs in the lab. There’s just one small setback: the organisms of interest come from some of our planet’s most extreme environments—environments that are quite difficult to replicate in a laboratory.

As the microbe-hunters of the group, OU researchers go to various extreme environments—hot springs, lakes ten times saltier than the ocean, sulfur springs with no measurable oxygen content and locations in the deep subsurface, miles below the earth—in search of methanotrophs.

“We don’t fully understand the flux of methane in these extreme environments,” said Abin. “These locations could be either a sink or a source of methane to the atmosphere. Little research has been devoted to understanding the microbes that inhabit these areas, so any samples we collect can be novel.”

At Sanford Lab, researchers traveled deep underground to collect samples from biofilms and groundwater from boreholes on the 4850 Level and sediments from the 1700 Level.

Christopher Abin sampling groundwater from a borehole on the 4850 Level of Sanford Lab. Photo courtesy Christopher Abin.

“We also collected a sample from an exotic fungus growing on a wooden beam,” Abin said. “You don’t really know going in what you’re going to find, so you sample everything you think might be interesting. You might discover something really cool when you analyze it back in the lab.”

During each excursion, the team takes two sets of samples. The first is dedicated to a DNA roll-call that identifies the hundreds—perhaps thousands—of species naturally present in that environment. The second set is dedicated to an advanced cultivation process in the lab, where researchers try to single out one or a few specific species through a process called enrichment.

“In the lab, we put our samples in bottles that can be sealed completely then add concentrations of gases like methane and oxygen at precise concentrations. As the methanotrophs consume methane, the concentration slowly decreases,” explained Abin.

Glass bottles containing s​​​​ediment samples incubating with methane and oxygen. Photo courtesy Christopher Abin.

Called a gas chromatograph, this instrument is used to measure methane in the glass bottles. Photo courtesy Christopher Abin.

“Once it is mostly depleted, we dilute the cultures to get rid of the background microbes we don’t want, achieving a higher proportion of just the methanotrophs,” said Abin. “We take a small amount of that liquid and place it onto a petri plate containing a semisolid material called agar to provide a substrate for the bacteria to grow on. As the bacteria grow, they produce visible colonies that we can purify further through a process called streaking.”

A petri plate with colonies of a methanotrophic microorganism growing on agar. Photo courtesy Christopher Abin.

At the end of the streaking process, researchers hope to isolate the single species from the multitudes present. Sometimes, however, organisms resist, preferring a more social environment.

“Species don’t grow in pure cultures in their natural environment,” said Rosie Moon-Escamilla, a graduate student at OU. “When two organisms exist together and provide benefits to each other, it’s difficult to make them survive without each other.”

If the methanotroph is growing in co-culture with another organism that is providing some sort of benefit to them, such as removing toxic substances or suppling a certain vitamin, the isolation process can get complicated.

“You do a lot of work to get the organism isolated, always knowing in the back of your mind that they are happier in co-culture,” said Moon-Escamilla. “Sometimes, it may not be impractical to isolate them into distinct pure cultures, it may be impossible.”

At the end of multiple rounds of streaking, if researchers have achieved a pure culture, they can begin to characterize them—What temperatures do they enjoy? Which solidities do they fancy?—to better understand the microbial preferences.

“The challenge of microbiology cultivation in general is how to replicate the environment you sample from,” said Christopher Garner, an OU graduate student. “We estimate that 90 percent of all microorganisms out there haven’t been cultivated in the lab, because it’s just something that’s really hard to do. When your samples are from an extreme environment, that adds additional challenges that makes it more difficult to cultivate.”

Collected from vastly differing locations, the physiology of these organisms varies—each suited to its own extreme environment—and each must be assessed and studied individually. The binding commonality, however, is that these organisms use methane as their energy source and have enormous potential in bioengineering applications.

Assorted methanotroph cultures in OU laboratory. Photo courtesy Christopher Abin.

“We’ve done a lot of work with media manipulation,” Moon-Escamilla said. “If you tailor the media to the specific location, being mindful of the salt and pH levels or different minerals present at each collection site, you have a better chance of increasing the number of microbes that will grow in the lab.”

A microscope and image of a methane-consuming microbial consortium from one of an enrichment culture in the OU lab. Photo courtesy Christopher Abin.

Much of the work involves experimentation, testing the conditions and letting the organism’s response inform the process.

“There is immense value in traditional microbiology work—cultivating microbes from the environment and learning about their metabolisms,” Garner said. “We’ve only begun to understand really how many different kinds of microbes there are out there.”

“The overarching goals of the BuG ReMeDEE consortium are to investigate methane cycling in deep and extreme environments and develop new biological routes for converting methane into value-added products,” said principal investigator Rajesh Sani. “Using ‘genome-to-phenome’ approaches, the consortium and will address critical regional, national and global issues of methane cycling, global warming, renewable energy and carbon neutrality.”

“This collaboration will allow our groups to synergistically solve problems that could not be dealt with alone. I feel strongly that our work on isolating and better understanding methanotrophs at SURF and other locations will allow us to better understand the fate of methane and its role as a greenhouse gas,” said Lee Krumholz, who leads the work being done at OU.

See the full article here .

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About us.
The Sanford Underground Research Facility in Lead, South Dakota, advances our understanding of the universe by providing laboratory space deep underground, where sensitive physics experiments can be shielded from cosmic radiation. Researchers at the Sanford Lab explore some of the most challenging questions facing 21st century physics, such as the origin of matter, the nature of dark matter and the properties of neutrinos. The facility also hosts experiments in other disciplines—including geology, biology and engineering.

The Sanford Lab is located at the former Homestake gold mine, which was a physics landmark long before being converted into a dedicated science facility. Nuclear chemist Ray Davis earned a share of the Nobel Prize for Physics in 2002 for a solar neutrino experiment he installed 4,850 feet underground in the mine.

Homestake closed in 2003, but the company donated the property to South Dakota in 2006 for use as an underground laboratory. That same year, philanthropist T. Denny Sanford donated $70 million to the project. The South Dakota Legislature also created the South Dakota Science and Technology Authority to operate the lab. The state Legislature has committed more than $40 million in state funds to the project, and South Dakota also obtained a $10 million Community Development Block Grant to help rehabilitate the facility.

In 2007, after the National Science Foundation named Homestake as the preferred site for a proposed national Deep Underground Science and Engineering Laboratory (DUSEL), the South Dakota Science and Technology Authority (SDSTA) began reopening the former gold mine.

In December 2010, the National Science Board decided not to fund further design of DUSEL. However, in 2011 the Department of Energy, through the Lawrence Berkeley National Laboratory, agreed to support ongoing science operations at Sanford Lab, while investigating how to use the underground research facility for other longer-term experiments. The SDSTA, which owns Sanford Lab, continues to operate the facility under that agreement with Berkeley Lab.

The first two major physics experiments at the Sanford Lab are 4,850 feet underground in an area called the Davis Campus, named for the late Ray Davis. The Large Underground Xenon (LUX) experiment is housed in the same cavern excavated for Ray Davis’s experiment in the 1960s.

LBNL LZ project at SURF, Lead, SD, USA, will replace LUX at SURF

In October 2013, after an initial run of 80 days, LUX was determined to be the most sensitive detector yet to search for dark matter—a mysterious, yet-to-be-detected substance thought to be the most prevalent matter in the universe. The Majorana Demonstrator experiment, also on the 4850 Level, is searching for a rare phenomenon called “neutrinoless double-beta decay” that could reveal whether subatomic particles called neutrinos can be their own antiparticle. Detection of neutrinoless double-beta decay could help determine why matter prevailed over antimatter. The Majorana Demonstrator experiment is adjacent to the original Davis cavern.

LUX’s mission was to scour the universe for WIMPs, vetoing all other signatures. It would continue to do just that for another three years before it was decommissioned in 2016.

In the midst of the excitement over first results, the LUX collaboration was already casting its gaze forward. Planning for a next-generation dark matter experiment at Sanford Lab was already under way. Named LUX-ZEPLIN (LZ), the next-generation experiment would increase the sensitivity of LUX 100 times.

SLAC physicist Tom Shutt, a previous co-spokesperson for LUX, said one goal of the experiment was to figure out how to build an even larger detector.
“LZ will be a thousand times more sensitive than the LUX detector,” Shutt said. “It will just begin to see an irreducible background of neutrinos that may ultimately set the limit to our ability to measure dark matter.”
We celebrate five years of LUX, and look into the steps being taken toward the much larger and far more sensitive experiment.

Another major experiment, the Long Baseline Neutrino Experiment (LBNE)—a collaboration with Fermi National Accelerator Laboratory (Fermilab) and Sanford Lab, is in the preliminary design stages. The project got a major boost last year when Congress approved and the president signed an Omnibus Appropriations bill that will fund LBNE operations through FY 2014. Called the “next frontier of particle physics,” LBNE will follow neutrinos as they travel 800 miles through the earth, from FermiLab in Batavia, Ill., to Sanford Lab.

FNAL LBNE/DUNE from FNAL to SURF, Lead, South Dakota, USA


U Washington Majorana Demonstrator Experiment at SURF

The MAJORANA DEMONSTRATOR will contain 40 kg of germanium; up to 30 kg will be enriched to 86% in 76Ge. The DEMONSTRATOR will be deployed deep underground in an ultra-low-background shielded environment in the Sanford Underground Research Facility (SURF) in Lead, SD. The goal of the DEMONSTRATOR is to determine whether a future 1-tonne experiment can achieve a background goal of one count per tonne-year in a 4-keV region of interest around the 76Ge 0νββ Q-value at 2039 keV. MAJORANA plans to collaborate with GERDA for a future tonne-scale 76Ge 0νββ search.

LBNL LZ project at SURF, Lead, SD, USA


CASPAR is a low-energy particle accelerator that allows researchers to study processes that take place inside collapsing stars.

The scientists are using space in the Sanford Underground Research Facility (SURF) in Lead, South Dakota, to work on a project called the Compact Accelerator System for Performing Astrophysical Research (CASPAR). CASPAR uses a low-energy particle accelerator that will allow researchers to mimic nuclear fusion reactions in stars. If successful, their findings could help complete our picture of how the elements in our universe are built. “Nuclear astrophysics is about what goes on inside the star, not outside of it,” said Dan Robertson, a Notre Dame assistant research professor of astrophysics working on CASPAR. “It is not observational, but experimental. The idea is to reproduce the stellar environment, to reproduce the reactions within a star.”